pre-built_references/colors.R

In immunogenomics/symphony: Efficient and Precise Single-Cell Reference Atlas Mapping

## Defines colors used for reference cell types plotting

pbmc_colors = c("B" = "#66C2A5", 
              "DC" = "#FC8D62",
              "HSC" = "#8DA0CB",
              "MK" = "#E78AC3", 
              "Mono_CD14" = "#A6D854",
              "Mono_CD16" = "#f2ec72",
              "NK" = "#62AAEA", 
              "T_CD4" = "#D1C656",
              "T_CD8" = "#968763")

pancreas_colors = c('alpha'="#ed2bb1",
                    'beta'="#239eb3",
                    'gamma'="#d1bfec",
                    'delta'= "#FF6347",
                    'stellate'="#11e38c",
                    'immune'="#812050",
                    'ductal'="#b2d27a",
                    'endothelial'="#4e2da6",
                    'acinar'="#f6bb86",
                    'schwann'="#115d52",
                    'epsilon'="#a1def0")

group.colors = c(   'B cell'='#f2bd80',
                    'DC precursor'='#1d6d1f',
                    'DC1'='#8c3ba0',
                    'DC2'='#6533ed',
                    'Early Erythroid'='#83e3f0',
                    'Early lymphoid/T'='#fd5917',
                    'Endothelial cell'='#4f8c9d',
                    'Fibroblast'='#eb1fcb',
                    'Hepatocyte'='#f5cdaf',
                    'HSC_MPP'='#9698dc',
                    'ILC precursor'='#20f53d',
                    'Kupffer Cell'='#f283e3',
                    'Late Erythroid'='#ffb2be',
                    'Mast cell'='#f3d426',
                    'Megakaryocyte'='#5ebf72',
                    'MEMP'='#a67649',
                    'Mid Erythroid'='#2f5bb1',
                    'Mono-Mac'='#90a479',
                    'Monocyte'='#f6932e',
                    'Monocyte precursor'='#d59e9a',
                    'Neut-myeloid prog.'='#caf243',
                    'NK'='#38b5fc',
                    'pDC precursor'='#c82565',
                    'Pre pro B cell'='#d6061a',
                    'pre-B cell'='#e36f6f',
                    'pro-B cell'='#1dfee1',
                    'VCAM1+ EI macro.'='#506356')

# Assorted colors
assort.colors = c(brewer.pal(name="Set1", n = 8), brewer.pal(name="Set2", n = 8),
             brewer.pal(name='Set3', n = 12),
             brewer.pal(name="Dark2", n = 8),
             brewer.pal(name='Accent', n = 7), 
             brewer.pal(name="Paired", n = 12),
             brewer.pal(name='Greens', n=4))

tms.colors = c(brewer.pal(name="Dark2", n = 8), brewer.pal(name="Paired", n = 12),
            brewer.pal(name="Set1", n = 9), brewer.pal(name="Set2", n = 8),
            brewer.pal(name='Accent', n = 7), brewer.pal(name='Set3', n = 12))